Variant report

Variant	rs10961672
Chromosome Location	chr9:14690419-14690420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:14686674..14691236-chr9:14691548..14694778,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175893	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10114225	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10125040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.85[EUR][1000 genomes]
rs10125223	0.96[EUR][1000 genomes]
rs10448192	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs10481506	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10756593	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[EUR][1000 genomes]
rs10756597	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap]
rs10756603	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10810211	1.00[CEU][hapmap];0.85[MEX][hapmap]
rs1114063	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1858635	1.00[CEU][hapmap];0.85[MEX][hapmap];0.80[MKK][hapmap]
rs2382476	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2382477	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2382491	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4469559	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4542027	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6474849	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7031629	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7035202	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs7039437	1.00[CEU][hapmap]
rs7850068	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7867569	1.00[CHB][hapmap]
rs7869713	0.92[EUR][1000 genomes]
rs7869716	0.92[EUR][1000 genomes]
rs7870354	0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9298701	1.00[CEU][hapmap]
rs9298704	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9298705	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9695032	0.92[EUR][1000 genomes]
rs9695276	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv831517	chr9:14512924-14738206	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3362157	chr9:14542189-14791977	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv521363	chr9:14566406-14691897	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv892605	chr9:14585052-14709151	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv892606	chr9:14588049-14697022	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv892609	chr9:14589173-14694302	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv2752921	chr9:14593749-14694372	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv892612	chr9:14654900-14694302	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv892613	chr9:14657139-14694302	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv6482	chr9:14673695-14718568	Enhancers Strong transcription ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1025566	chr9:14687088-14791199	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv613645	chr9:14687455-14690419	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14631000-14692400	Weak transcription	HSMMtube	muscle
2	chr9:14634600-14692400	Weak transcription	Gastric	stomach
3	chr9:14634600-14692600	Weak transcription	Aorta	Aorta
4	chr9:14654200-14692600	Weak transcription	Pancreas	Pancrea
5	chr9:14655200-14690600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:14655400-14690600	Weak transcription	Brain Angular Gyrus	brain
7	chr9:14655400-14690600	Weak transcription	Fetal Kidney	kidney
8	chr9:14655400-14691000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:14655400-14691400	Weak transcription	A549	lung
10	chr9:14655400-14692200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr9:14655600-14692200	Weak transcription	Fetal Lung	lung
12	chr9:14655800-14692200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:14656000-14692400	Weak transcription	Colonic Mucosa	Colon
14	chr9:14656200-14692400	Weak transcription	Primary T cells from cord blood	blood
15	chr9:14657000-14692600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:14659600-14692400	Weak transcription	Colon Smooth Muscle	Colon
17	chr9:14660200-14691000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:14663400-14692000	Weak transcription	Brain Substantia Nigra	brain
19	chr9:14670800-14692200	Weak transcription	NHLF	lung
20	chr9:14671200-14692000	Weak transcription	HepG2	liver
21	chr9:14671600-14692200	Weak transcription	NHEK	skin
22	chr9:14672600-14692400	Weak transcription	Small Intestine	intestine
23	chr9:14672800-14692200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr9:14675400-14692400	Weak transcription	Ovary	ovary
25	chr9:14676800-14692200	Weak transcription	Fetal Brain Female	brain
26	chr9:14678400-14690800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr9:14678800-14692200	Weak transcription	Liver	Liver
28	chr9:14679200-14691000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:14680200-14692200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr9:14681400-14692600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:14681800-14691000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr9:14681800-14692200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:14682000-14692600	Weak transcription	Spleen	Spleen
34	chr9:14685000-14692400	Weak transcription	Right Ventricle	heart
35	chr9:14685800-14691000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr9:14685800-14692400	Weak transcription	Thymus	Thymus
37	chr9:14686200-14690800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:14686200-14691000	Weak transcription	Dnd41	blood
39	chr9:14686200-14692400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr9:14686600-14692000	Weak transcription	Stomach Mucosa	stomach
41	chr9:14686800-14692400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr9:14687200-14691000	Weak transcription	Brain Hippocampus Middle	brain
43	chr9:14687200-14691400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr9:14687200-14692600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr9:14687400-14692200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr9:14687600-14691000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr9:14687600-14691400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:14687600-14692000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr9:14687600-14692400	Weak transcription	Psoas Muscle	Psoas
50	chr9:14687600-14692600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links